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The Scientific Method and Historical Perspectives in Microbiology . Science. “ All reasoning is thinking, but not all thinking is reasoning”-Irving Copi. Science is a systematic way of gaining knowledge and endeavors to eliminate bias

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The Scientific Method and Historical Perspectives in Microbiology

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“ All reasoning is thinking, but not all thinking is reasoning”-Irving Copi

  • Science is a systematic way of gaining knowledge and endeavors to eliminate bias
  • It is based on branch of philosophy that deals with logic and cannot answer questions beyondreason or beyond the natural world (i.e. metaphysical questions)
  • Unscientific thought is dogmatic (not based on proof). It is often based in belief in an absolute truth without possibility of modification or correction
  • Scientific propositions are regarded as hypotheses (theory and law are often misleading terms; they are refined hypotheses that are repeatedly supported by scientific observation)
scientific propositions
Scientific Propositions

Hypothesis- an unproven proposition based on observation

Theory- a proposition that has been supported by scientific testing and observable facts (organic evolution, heredity, cell, gene)

Law- a proposition that is invariably supported when tested (e.g. gravity, thermodynamics)

All must be testable and are never dogmas or absolute truths

the scientific method
The Scientific Method
  • Make observation
  • Form a hypothesis
  • Design a controlled experiment
  • Evaluate data (test assumptions, assess variability etc…)
  • Repeat or refine experiment


Propose Hypothesis

Propose Alternate Hypothesis

Design Experiment

Collect and Analyze Data

Redesign Experiment

Not repeatable

Determine if Data are Bias

Data are Bias

Refine Hypothesis

Repeat Experiment


Accept as Theory

causes and correlations
Causes and Correlations
  • Observing a correlation indicates a relationship exists between two variables
  • It does not imply that either of the variables causes the other
  • Correlational studies are valuable in the beginning stages of scientific investigations but require further investigation to demonstrate causality
direct positive correlation
Direct (positive) Correlation

Observed disease symptoms

Presence of microbe in patients

inverse negative correlation
Inverse (negative) Correlation

Observed disease symptoms

Immune system activity

  • The science of cause is etiology
  • In science- it refers to a necessary and sufficient condition
  • Careful not to use imprecisely
    • Ex: cold virus is the cause of nasal congestion
  • Can be classified as either proximate or remote causes

AB  C  D  E

  • A is a remote cause of E
  • D is a proximate cause of E
  • Etiological agents are the causative agents of disease
  • Koch’s postulates are used to prove that a specific agent is the cause of a particular
using science to identify the etiological agents of disease
Using science to identify the etiological agents of disease
  • Signs and symptoms are indications that the body is sick, they are important observations in forming a hypothesis regarding the etiology of infectious disease
    • H: Agent X is the cause of the signs or symptoms
  • Diagnosing a disease doesn’t necessarily reveal the etiological agent
    • Some diseases are caused by more than one agent e.g. meningitis, pneumonia, wound infection
  • Indirect identification includes the use of signs or antibodies specific to the agent
  • Direct identification relies on observing the agent and its characteristics
robert koch
Robert Koch
  • Koch identified causative agents of diseases such as anthrax and tuberculosis
  • Introduced pure culture techniques
koch s postulates
Koch’s Postulates
  • The specific cause must be found in every case of the disease
  • The disease organism must be isolated in a pure culture
  • Inoculation of organism into healthy animal must produce the same disease
  • The disease organism must be recovered from the inoculated animal
koch s postulates1
Koch’s Postulates



Culture the agent


Isolate each type of organism in a pure culture

designing an experiment
Designing an Experiment

Designing a scientific experiment to test the hypothesis that agent X is the cause of disease

Inoculate Treatment Group with agent X (suspected pathogen)

Inoculate Control Group with agent Z (not harmful) as a standard for comparison


What do the results suggest?


# of rats



asymptomatic rats

diseased rats

how important are koch s postulates
How important are Koch’s postulates?
  • Koch’s postulates have not been satisfied for all organisms that we consider to be pathogenic
  • Remember that science does not deal with absolute truths and there are many factors that contribute to disease besides the agent
  • As we learn more about pathogens and hosts and the relationships between them from a scientific perspective, we are more likely to prevent and treat infectious disease
  • Many diseases actually result from homeostatic imbalance and therefore microorganismsare cofactors rather than etiological agents
taxonomy systematics
  • The scientist Linnaeus (1707-1778) sought to classify organisms in an organized way to more easily study and keep track of them.
  • He also practiced medicine and specialized in syphilis
  • His method of binomial nomenclature utilizes Latinized names for groups of related organisms
  • The groups names most often used to identify organisms are genus and species
  • The genus and species names are italicized or underlined.
  • The genus name is capitalized and the species name is not.

Example: Escherichia coli

modern taxonomy systematics reflects evolutionary relationships
Modern taxonomy (systematics) reflects evolutionary relationships

Charles Darwin’s inquiries led to a chain reaction of scientific breakthroughs in biology

The rapid evolution of microbes provides clear scientific evidence for evolution, but presents a great challenge to public health

antibiotic resistance

antigenic shift and drift

host-parasite coevolution


Taxonomic Classification

Domains- Archaea, Bacteria, Eukarya

Kingdom- there are currently five or six kingdoms depending on how you slice them (viruses not included)






Species-there are millions of species

Subspecies are also recognized

  • Five Kingdoms:
  • Animalia
  • Plantae
  • Fungi
  • Protista
  • Monera (Archaea, Bacteria)
why is taxonomy systematics important in microbiology and human disease
Why is taxonomy/systematics important in microbiology and human disease?

Suspect organism is cause of a new disease

Organism is new species

Can be placed into group that is most similar

Can make testable hypotheses about new species based on similarity to known groups

Family tree of known organisms

percentage of shared characteristics
Percentage of Shared Characteristics





Revised family tree

historical perspectives
Historical Perspectives
  • History provides us with many good examples of the scientific method
  • The study of history itself can be studied scientifically
  • Knowledge of history gives us hindsight
  • History reminds us of what is possible in the future
classic microbiology
Classic Microbiology

Food Production





Leading Causes of Death in U.S, CDC 2002

As of 2006 Alzheimer’s Deaths surpassed influenza

the black death in europe ca 1300s
The Black Death in Europe ca.1300s

While outbreaks of plague occurred around the world throughout recorded history, there were three major pandemics: Justinian plague(500s A.D), black death( 1300s) and modern (1900s).

The black death occurred during mediaeval times and killed millions

timeline of historical events and people
Timeline of Historical Events and People

1546 A.D.-Italian Physician Girolamo Fracastro Suggests that invisible organisms cause disease

1665-Robert Hooke publishes his observations of cells in cork

Late 1600s-Francesco Redi tests the “theory” of spontaneous generation

anton van leeuvenhoek
Anton van Leeuvenhoek
  • 1677-Observed microorganisms which he called ‘animacules’
edward jenner
Edward Jenner

1796- discovered small pox vaccine (vacca=cow)

This was before viruses were know as etiological agents of disease

He noticed that milk maids who had cow pox (vaccinia virus) scars were resistant to small pox

the golden age of microbiology
The “Golden Age” of Microbiology

1840-J. Henle exposes germ theory of disease

1847-1850 Ignaz Semmelweis suggests hand washing to prevent childbed fever

1853-John Snow demonstrates the spread of cholera through contaminated water

1857-1860s-Pasteur’s work refutes spontaneous generation, he invents pasteurization, shows CO2 production in yeast

1862- Joseph Lister practiced antiseptic surgery

the 1900s
The 1900s

1908-Paul Ehrlich develops drug to treat syphilis

1928-Griffith discovers genetic transformation in bacteria

1929-Alexander Fleming discovers penicillin

1943-Luria and Delbruck demonstrate randomness of mutations that confer antibiotic resistance

1948-Barbara McClintock demonstrates transposable elements

1953-Crick and Watson crack genetic code

1973-Boyer and Cohen clone DNA using plasmid

1981-Stanely Prusiner discovers prions

1983-Kery Mullis invents PCR

1995-First complete bacteria genome sequenced

21 st century microbiology
21st century microbiology

2001-Anthrax attack in USA, huge increase in funding for biodefense research

2003-SARS epidemic

2005-chicken pox vaccine

2006-HPV vaccine

2007-Avian influenza vaccine